{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T10:28:25Z","timestamp":1789122505822,"version":"build-2803163510"},"reference-count":32,"publisher":"Microbiology Society","issue":"12","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,12,1]]},"abstract":"<jats:p>Eight bacterial strains isolated from the caecum of chicken, BL2<jats:sup>T<\/jats:sup>, BL66, EG3, EG6, M27, BL78<jats:sup>T<\/jats:sup>, C35<jats:sup>T<\/jats:sup>and C43, were characterized by determining their phenotypic characteristics, cellular fatty acid profiles, menaquinone profiles and phylogenetic positions based on 16S rRNA gene sequence analysis. 16S rRNA gene sequence analysis showed that these isolates belonged to the genus<jats:italic>Bacteroides<\/jats:italic>. One group of five strains (BL2<jats:sup>T<\/jats:sup>, BL66, EG3, EG6 and M27) was related most closely to<jats:italic>Bacteroides coprocola<\/jats:italic>JCM 12979<jats:sup>T<\/jats:sup>, with approximately 93\u200a% 16S rRNA gene sequence similarity, and to<jats:italic>Bacteroides plebeius<\/jats:italic>JCM 12973<jats:sup>T<\/jats:sup>, with about 92\u200a% similarity, and shared \u2a7e99.6\u200a% similarity with each other. Strain BL78<jats:sup>T<\/jats:sup>exhibited 90.5\u200a% similarity to<jats:italic>B. plebeius<\/jats:italic>JCM 12973<jats:sup>T<\/jats:sup>and 89.8\u200a% similarity to<jats:italic>B. coprocola<\/jats:italic>JCM 12979<jats:sup>T<\/jats:sup>and differed from the above group of five strains at \u2a7e10\u200a% sequence divergence. Strains C35<jats:sup>T<\/jats:sup>and C43 were related most closely to<jats:italic>Bacteroides eggerthii<\/jats:italic>JCM 12986<jats:sup>T<\/jats:sup>, with 95.1\u200a% sequence similarity, to<jats:italic>Bacteroides stercoris<\/jats:italic>JCM 9496<jats:sup>T<\/jats:sup>, with 94.6\u200a% similarity, and to<jats:italic>Bacteroides uniformis<\/jats:italic>JCM 5828<jats:sup>T<\/jats:sup>, with 94.4\u200a% similarity, and shared 100\u200a% similarity with each other. From results of phenotypic examination, cellular fatty acid composition analysis, menaquinone composition analysis and DNA G+C contents, the group of five strains as well as strain BL78<jats:sup>T<\/jats:sup>were shown to differ from the type strains of<jats:italic>B. coprocola<\/jats:italic>and<jats:italic>B. plebeius<\/jats:italic>. Strain BL78<jats:sup>T<\/jats:sup>differed from the others based on its menaquinone composition, which included MK-11 and MK-12. Strains C35<jats:sup>T<\/jats:sup>and C43 could also be differentiated from the type strains of<jats:italic>B. eggerthii<\/jats:italic>,<jats:italic>B. stercoris<\/jats:italic>and<jats:italic>B. uniformis<\/jats:italic>. The group of five strains, strain BL78<jats:sup>T<\/jats:sup>,<jats:italic>B. coprocola<\/jats:italic>JCM 12979<jats:sup>T<\/jats:sup>and<jats:italic>B. plebeius<\/jats:italic>JCM 12973<jats:sup>T<\/jats:sup>showed low levels of DNA\u2013DNA relatedness (&lt;35\u200a%) with each other. High levels of DNA\u2013DNA relatedness were obtained within the group of five strains (&gt;75\u200a%). Strains C35<jats:sup>T<\/jats:sup>and C43 exhibited a high level of DNA\u2013DNA relatedness (&gt;88\u200a%) with each other, but low levels with<jats:italic>B. eggerthii<\/jats:italic>JCM 12986<jats:sup>T<\/jats:sup>(&lt;40\u200a%),<jats:italic>B. stercoris<\/jats:italic>JCM 9496<jats:sup>T<\/jats:sup>(&lt;37\u200a%) and<jats:italic>B. uniformis<\/jats:italic>JCM 5828<jats:sup>T<\/jats:sup>(&lt;16\u200a%). On the basis of these data, three novel<jats:italic>Bacteroides<\/jats:italic>species are proposed:<jats:italic>Bacteroides barnesiae<\/jats:italic>sp. nov. (type strain BL2<jats:sup>T<\/jats:sup>=JCM 13652<jats:sup>T<\/jats:sup>=DSM 18169<jats:sup>T<\/jats:sup>),<jats:italic>Bacteroides salanitronis<\/jats:italic>sp. nov. (type strain BL78<jats:sup>T<\/jats:sup>=JCM 13657<jats:sup>T<\/jats:sup>=DSM 18170<jats:sup>T<\/jats:sup>) and<jats:italic>Bacteroides gallinarum<\/jats:italic>sp. nov. (type strain C35<jats:sup>T<\/jats:sup>=JCM 13658<jats:sup>T<\/jats:sup>=DSM 18171<jats:sup>T<\/jats:sup>).<\/jats:p>","DOI":"10.1099\/ijs.0.64517-0","type":"journal-article","created":{"date-parts":[[2006,12,11]],"date-time":"2006-12-11T23:22:50Z","timestamp":1165879370000},"page":"2853-2859","source":"Crossref","is-referenced-by-count":85,"title":["Bacteroides barnesiae sp. nov., Bacteroides salanitronis sp. nov. and Bacteroides gallinarum sp. nov., isolated from chicken caecum"],"prefix":"10.1099","volume":"56","author":[{"given":"Pham Thi Ngoc","family":"Lan","sequence":"first","affiliation":[{"name":"Microbe Division\/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan"},{"name":"Institute of Biotechnology, Vietnamese Academy of Science and Technology, Hanoi, Vietnam"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mitsuo","family":"Sakamoto","sequence":"additional","affiliation":[{"name":"Microbe Division\/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shinji","family":"Sakata","sequence":"additional","affiliation":[{"name":"Microbe Division\/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yoshimi","family":"Benno","sequence":"additional","affiliation":[{"name":"Microbe Division\/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","first-page":"89","article-title":"Analysis of the avian intestinal flora","author":"Barnes","year":"1978","journal-title":"In Techniques for the Study of Mixed Populations , Society for Applied Bacteriology Technical Series no. \u200511"},{"key":"R2","doi-asserted-by":"crossref","first-page":"794","DOI":"10.1128\/AEM.14.5.794-801.1966","article-title":"Medium without rumen fluid for nonselective enumeration and isolation of rumen bacteria","volume":"14","author":"Caldwell","year":"1966","journal-title":"Appl Microbiol"},{"key":"R3","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1128\/MMBR.45.2.316-354.1981","article-title":"Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implications","volume":"45","author":"Collins","year":"1981","journal-title":"Microbiol Rev"},{"key":"R4","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1007\/s002849900184","article-title":"Starch utilization by Bacteroides ovatus isolated from the human large intestine","volume":"34","author":"Degnan","year":"1997","journal-title":"Curr Microbiol"},{"key":"R5","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1099\/00207713-39-3-224","article-title":"Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains","volume":"39","author":"Ezaki","year":"1989","journal-title":"Int J Syst Bacteriol"},{"key":"R6","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1111\/j.1558-5646.1985.tb00420.x","article-title":"Confidence limits of phylogenies: an approach using the bootstrap","volume":"39","author":"Felsenstein","year":"1985","journal-title":"Evolution"},{"key":"R7","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1016\/B978-0-12-341280-5.50020-3","article-title":"Role of the intestinal flora in host defense against infection","volume-title":"In Human Intestinal Microflora in Health and Disease","author":"Hentges","year":"1983"},{"key":"R8","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/B978-0-12-256745-2.50007-6","article-title":"Anaerobes as normal flora","volume-title":"In Anaerobic Infections in Humans","author":"Hentges","year":"1989"},{"key":"R9","volume-title":"Anaerobe Laboratory Manual","author":"Holdeman","year":"1977"},{"key":"R10","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1007\/BF01731581","article-title":"A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences","volume":"16","author":"Kimura","year":"1980","journal-title":"J Mol Evol"},{"key":"R11","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1016\/S0580-9517(08)70410-0","article-title":"Lipid and cell-wall analysis in bacterial systematics","volume":"19","author":"Komagata","year":"1987","journal-title":"Methods Microbiol"},{"key":"R12","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1099\/00207713-38-4-358","article-title":"Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum","volume":"38","author":"Kuykendall","year":"1988","journal-title":"Int J Syst Bacteriol"},{"key":"R13","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1111\/j.1348-0421.2002.tb02709.x","article-title":"Phylogenetic analysis of cecal microbiota in chicken by the use of 16S rDNA clone libraries","volume":"46","author":"Lan","year":"2002","journal-title":"Microbiol Immunol"},{"key":"R14","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1016\/S0022-2836(61)80047-8","article-title":"A procedure for the isolation of deoxyribonucleic acid from microorganisms","volume":"3","author":"Marmur","year":"1961","journal-title":"J Mol Biol"},{"key":"R15","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1099\/00207713-32-1-21","article-title":"Identification of Bacteroides species by cellular fatty acid profiles","volume":"32","author":"Mayberry","year":"1982","journal-title":"Int J Syst Bacteriol"},{"key":"R16","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1128\/JCM.16.3.584-586.1982","article-title":"Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids","volume":"16","author":"Miller","year":"1982","journal-title":"J Clin Microbiol"},{"key":"R17","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1111\/j.1348-0421.1969.tb00482.x","article-title":"A simple method (\u201cplate-in-bottle method\u201d) for the cultivation of fastidious anaerobes","volume":"13","author":"Mitsuoka","year":"1969","journal-title":"Jpn J Microbiol"},{"key":"R18","doi-asserted-by":"crossref","first-page":"41","DOI":"10.2323\/jgam.25.41","article-title":"Cellular fatty acid composition in gram-negative obligately anaerobic rods","volume":"25","author":"Miyagawa","year":"1979","journal-title":"J Gen Appl Microbiol"},{"key":"R19","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1128\/JB.179.3.643-649.1997","article-title":"Characterization of four outer membrane proteins that play a role in utilization of starch by Bacteroides thetaiotaomicron","volume":"179","author":"Reeves","year":"1997","journal-title":"J Bacteriol"},{"key":"R20","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1016\/0926-6550(63)90386-4","article-title":"Preparation of transforming deoxyribonucleic acid by phenol treatment","volume":"72","author":"Saito","year":"1963","journal-title":"Biochim Biophys Acta"},{"key":"R21","first-page":"406","article-title":"The neighbor-joining method: a new method for reconstructing phylogenetic trees","volume":"4","author":"Saitou","year":"1987","journal-title":"Mol Biol Evol"},{"key":"R22","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1099\/00207713-52-3-841","article-title":"Reclassification of Bacteroides forsythus (Tanner et al . 1986) as Tannerella forsythensis corrig., gen","volume":"52","author":"Sakamoto","year":"2002","journal-title":"nov., comb. nov. Int J Syst Evol Microbiol"},{"key":"R23","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1099\/ijs.0.02876-0","article-title":"Prevotella shahii sp. nov. and Prevotella salivae sp. nov., isolated from the human oral cavity","volume":"54","author":"Sakamoto","year":"2004","journal-title":"Int J Syst Evol Microbiol"},{"key":"R24","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1099\/ijs.0.63451-0","article-title":"Prevotella multiformis sp. nov., isolated from human subgingival plaque","volume":"55","author":"Sakamoto","year":"2005","journal-title":"Int J Syst Evol Microbiol"},{"key":"R25","doi-asserted-by":"crossref","first-page":"678","DOI":"10.1128\/AEM.27.4.678-687.1974","article-title":"Isolation, culture characteristics, and identification of anaerobic bacteria from the chicken cecum","volume":"27","author":"Salanitro","year":"1974a","journal-title":"Appl Microbiol"},{"key":"R26","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1128\/AEM.28.3.439-447.1974","article-title":"Studies on the cecal microflora of commercial broiler chickens","volume":"28","author":"Salanitro","year":"1974b","journal-title":"Appl Microbiol"},{"key":"R27","doi-asserted-by":"crossref","first-page":"3593","DOI":"10.1007\/978-1-4757-2191-1_34","article-title":"The genus Bacteroides and related taxa","volume-title":"In The Prokaryotes","author":"Shah","year":"1992"},{"key":"R28","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1111\/j.1365-2672.1980.tb05209.x","article-title":"Fatty acid and isoprenoid quinone composition in the classification of Bacteroides melaninogenicus and related taxa","volume":"48","author":"Shah","year":"1980","journal-title":"J Appl Bacteriol"},{"key":"R29","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1111\/j.1365-2672.1983.tb01680.x","article-title":"Genus Bacteroides . A chemotaxonomical perspective","volume":"55","author":"Shah","year":"1983","journal-title":"J Appl Bacteriol"},{"key":"R30","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1111\/j.1574-6968.1984.tb01388.x","article-title":"Determination of DNA base composition by reversed-phase high-performance liquid chromatography","volume":"25","author":"Tamaoka","year":"1984","journal-title":"FEMS Microbiol Lett"},{"key":"R31","doi-asserted-by":"crossref","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","article-title":"clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice","volume":"22","author":"Thompson","year":"1994","journal-title":"Nucleic Acids Res"},{"key":"R32","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1017\/S0022172400021653","article-title":"Colonization resistance of the digestive tract in conventional and antibiotic-treated mice","volume":"69","author":"van der Waaij","year":"1971","journal-title":"J Hyg"}],"container-title":["International Journal of Systematic and Evolutionary Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/ijsem\/10.1099\/ijs.0.64517-0?crawler=true","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,12]],"date-time":"2025-01-12T08:55:33Z","timestamp":1736672133000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/ijsem\/10.1099\/ijs.0.64517-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,12,1]]},"references-count":32,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2006,12,1]]}},"URL":"https:\/\/doi.org\/10.1099\/ijs.0.64517-0","relation":{},"ISSN":["1466-5026","1466-5034"],"issn-type":[{"value":"1466-5026","type":"print"},{"value":"1466-5034","type":"electronic"}],"subject":[],"published":{"date-parts":[[2006,12,1]]}}}